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- PDB-1mjj: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGM... -

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Basic information

Entry
Database: PDB / ID: 1mjj
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION-STATE ANALOG
Components(IMMUNOGLOBULIN MS6-12) x 2
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HAL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsRuzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. ...Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity
Authors: Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue
Authors: Muranova, T.A. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Moir, A. / Partridge, L.J. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_database_remark ...entity_poly / pdbx_database_remark / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_remark.text ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_remark.text / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN MS6-12
B: IMMUNOGLOBULIN MS6-12
L: IMMUNOGLOBULIN MS6-12
H: IMMUNOGLOBULIN MS6-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3729
Polymers97,1314
Non-polymers1,2415
Water16,448913
1
A: IMMUNOGLOBULIN MS6-12
B: IMMUNOGLOBULIN MS6-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3306
Polymers48,5652
Non-polymers7654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-57 kcal/mol
Surface area18690 Å2
MethodPISA
2
L: IMMUNOGLOBULIN MS6-12
H: IMMUNOGLOBULIN MS6-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0423
Polymers48,5652
Non-polymers4761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.281, 93.841, 142.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN MS6-12


Mass: 24191.900 Da / Num. of mol.: 2 / Fragment: Fab fragment, LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: fusing of mouse splenocytes with myeloma cell / Cell line: hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody IMMUNOGLOBULIN MS6-12


Mass: 24373.428 Da / Num. of mol.: 2 / Fragment: Fab fragment, HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: fusing of mouse splenocytes with myeloma cell / Cell line: hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HAL / N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE


Mass: 476.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, Ammonium sulphate, Sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(w/v)PEG40001reservoir
20.2 M1reservoirMgCl2
30.1 MTris-HCl1reservoirpH8.5
420 %PEG33501reservoir
50.2 Mpotassium thiocyanate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 50305 / Num. obs: 50305 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3 / % possible all: 49.5
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 49.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1MH5

1mh5


Resolution: 2.1→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2555 2707 RANDOM
Rwork0.1784 --
all-50305 -
obs-50305 -
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 0 81 913 7570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.66854
X-RAY DIFFRACTIONc_bond_d0.009621
X-RAY DIFFRACTIONc_mcbond_it4.9423.5
X-RAY DIFFRACTIONc_scbond_it7.2824
X-RAY DIFFRACTIONc_mcangle_it6.0584
X-RAY DIFFRACTIONc_scangle_it8.5894.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4hap.param
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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